Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant.

BACKGROUND: MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the two main types of non-coding RNAs that play crucial roles in plant growth and development. However, their specific roles in the fiber growth of ramie plant (Boehmeria nivea L. Gaud) remain largely unknown. METHODS: In this study, we performed miRNA and whole-transcriptome sequencing of two stem bark sections exhibiting different fiber growth stages to determine the expression profiles of miRNAs, lncRNAs, and protein-encoding genes. RESULTS: Among the identified 378 miRNAs and 6,839 lncRNAs, 88 miRNAs and 1,288 lncRNAs exhibited differential expression. Bioinformatics analysis revealed that 29 and 228 differentially expressed protein-encoding genes were targeted by differentially expressed miRNAs and lncRNAs, respectively, constituting eight putative competing endogenous RNA networks. lncR00022274 exhibited downregulated expression in barks with growing fibers. It also had an antisense overlap with the MYB gene, BntWG10016451, whose overexpression drastically increased the xylem fiber number and secondary wall thickness of fibers in the stems of transgenic Arabidopsis, suggesting the potential association of lncR00022274-BntWG10016451 expression with fiber growth. CONCLUSIONS: These findings provide insights into the roles of ncRNAs in the regulation of fiber growth in ramie, which can be used for the biotechnological improvement of its fiber yield and quality in the future.

Enhanced degradation of perfluorooctanoic acid by a genome shuffling-modified Pseudomonas parafulva YAB-1.

Perfluorooctanoic acid (PFOA) as an emerging persistent organic pollutant is hard to be degraded by conventional methods because of its stable physical and chemical properties. Microbial transformation is an attractive remediation approach to prevent and clean up PFOA contamination. To date, several strains of wild microbes have been reported to have limited capacity to degrade PFOA, selection of superior strains degrading PFOA become urgently necessary. Here, we report the application of genome shuffling to improve the PFOA-degrading bacterium Pseudomonas Parafulva YAB-1. The initial mutant populations of strain YAB1 were generated by nitrosoguanidine and ultraviolet irradiation mutagenesis respectively, resulting in mutants YM-9 and YM-19 with slightly improved PFOA-degrading ability. YM-9 and YM-19 were used as the starting strains for three rounds of recursive protoplast fusion. The positive mutants were screened on inorganic salt medium plates containing different concentrations of PFOA and selected based on their PFOA degradability in shake-flask fermentation test. The best performing recombinant F3-52 was isolated after three rounds of genome shuffling. In batch fermentation, the PFOA degradation rate of mutant F3-52 was up to 58.6%, which was 1.8-fold higher than that of the parent strain YAB1, and 1.6-fold higher than the initial mutants YM-9 and YM-19. Pass-generation test indicated that the heredity character of F3-52 was stable. The results demonstrated that genome shuffling was an efficient method for improving PFOA degradation of Pseudomonas Parafulva YAB1. The bred mutant F3-52 with 58.6% PFOA-degrading rate could be used for the environmental control of PFOA pollutant.

Draft Genome Sequence of the Vanadium-Leaching Bacterium Pseudomonas chlororaphis Strain L19.

Pseudomonas chlororaphis strain L19, isolated from stone coal soil, has the ability to perform bioleaching to release vanadium ions from mineral ore. Here, we report the draft genome sequence and annotation of the vanadium-leaching bacterium Pseudomonas chlororaphis L19. These data provide information for understanding the genomic properties and mineral bioleaching mechanisms of strain L19.

Draft Genome Sequence of the Potassium Feldspar-Solubilizing Bacterium Ensifer adhaerens L18.

Ensifer adhaerens L18, isolated from potassium feldspar mining area soil, was found to be capable of solubilizing K from an insoluble K-bearing mineral source. Here, we report the draft genome sequence and annotation of the feldspar-solubilizing bacterium Ensifer adhaerens L18. These data provide the basis to investigate the relative impact of bacteria in feldspar solubilizing and the molecular mechanism of the potassium feldspar's dissolution.

Draft Genome Sequence of Perfluorooctane Acid-Degrading Bacterium Pseudomonas parafulva YAB-1.

Pseudomonas parafulva YAB-1, isolated from perfluorinated compound-contaminated soil, has the ability to degrade perfluorooctane acid (PFOA) compound. Here, we report the draft genome sequence and annotation of the PFOA-degrading bacterium P. parafulva YAB-1. The data provide the basis to investigate the molecular mechanism of PFOA metabolism.

Pontibacillus litoralis sp. nov., a facultatively anaerobic bacterium isolated from a sea anemone, and emended description of the genus Pontibacillus.

A facultatively anaerobic, moderately halophilic, Gram-positive, endospore-forming, motile, catalase- and oxidase-positive, rod-shaped bacterium, strain JSM 072002(T), was isolated from a sea anemone (Anthopleura xanthogrammica) collected from the South China Sea. Strain JSM 072002(T) was able to grow with 0.5-15 % (w/v) NaCl and at pH 6.0-10.0 and 15-50 degrees C; optimum growth was observed with 2-5 % (w/v) NaCl and at pH 7.5 and 35 degrees C. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). The predominant respiratory quinone was menaquinone 7 and the genomic DNA G+C content was 41.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 072002(T) should be assigned to the genus Pontibacillus and revealed relatively low 16S rRNA gene sequence similarities (<97 %) with the type strains of the three recognized Pontibacillus species (Pontibacillus chungwhensis BH030062(T), 96.8 %; Pontibacillus marinus KCTC 3917(T), 96.7 %; Pontibacillus halophilus JSM 076056(T), 96.0 %). The combination of phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the view that strain JSM 072002(T) represents a novel species of the genus Pontibacillus, for which the name Pontibacillus litoralis sp. nov. is proposed. The type strain is JSM 072002(T) (=DSM 21186(T)=KCTC 13237(T)). An emended description of the genus Pontibacillus is also presented.

Pontibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from a sea urchin.

A Gram-positive-staining, moderately halophilic, strictly aerobic, catalase- and oxidase-positive, rod-shaped bacterium, designated strain JSM 076056(T), was isolated from a sea urchin collected from the South China Sea. Cells were motile by means of peritrichous flagella and formed ellipsoidal endospores lying in subterminal swollen sporangia. Strain JSM 076056(T) was able to grow at salinities of 2-25 % (w/v) total salts and at pH 6.0-10.0 and 15-40 degrees C; optimum growth was observed with 5-10 % (w/v) total salts and at pH 7.0-8.0 and 25-30 degrees C. It was incapable of growing with NaCl as the sole salt. meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C(15 : 0), iso-C(16 : 0), iso-C(14 : 0,) anteiso-C(15 : 0) and C(16 : 1)omega7c alcohol. The predominant respiratory quinone was MK-7 and the genomic DNA G+C content was 45.5 mol%. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 076056(T) belonged to the family Bacillaceae and was related most closely to the type strains of the two recognized species of the genus Pontibacillus, namely Pontibacillus chungwhensis BH030062(T) (96.4 % sequence similarity) and Pontibacillus marinus BH030004(T) (96.2 %); these three strains formed a robust cluster in the phylogenetic tree. In combination, the phylogenetic, phenotypic and chemotaxonomic data indicate that strain JSM 076056(T) represents a novel species of the genus Pontibacillus, for which the name Pontibacillus halophilus sp. nov. is proposed. The type strain is JSM 076056(T) (=CCTCC AA 207029(T) =DSM 19796(T) =KCTC 13190(T)).

[Phylogenetic diversity of cultivable bacteria associated with a sea anemone from coast of the Naozhou island in Zhanjiang, China].

OBJECTIVE: To understand the diversity of cultivable bacteria isolated from a sea anemone collected from the coastal water of the Naozbou island in the Leizhou Bay on South China Sea. METHODS: Bacteria were isolated from a sea anemone by using conventional culture-dependent method and investigated by using phylogenetic analysis based on 165 rRNA gene sequence comparisons. RESULTS: We isolated 126 bacteria strains from the sample on marine agar 2216 (Difco), International Streotomyces Project medium 2 agar, nutrient agar, sea water agar and humic acid agar supplemented with 0-2 mol/L NaCl. Based on partial morphological, physiological and biochemical characteristics, we selected 42 strains for molecular systematic study based on 16S rRNA gene sequences. Our results showed that 42 isolates were members of eighteen genera (Alteromonas, Bacillus, Brachybacterium, Brevibacterium, Halobacillus, Halomonas, Nocardiopsis, Oceanobacillus, Piscibacillus, Planococcus, Pontibacillus, Pseudoalteromonas, Pseudonocardia, Salinicoccus, Salinivibrio, Staphylococcus, Vibrio, Virgibacillus) of eleven families (Alteromonadaceae, Bacillaceae, Brevibacteriaceae, Dermabacteraceae, Halomonadaceae, Planococcaceae, Pseudoalteromonadaceae, Pseudonocardiaceae, Nocardiopsaceae, Staphylococcaceae, Vibrionaceae) in three major phylogenetic groups (Actinobacteria, Firmicutes, Gamma-Proteobacteria). The most abundant and diverse isolates were within the phylum Firmicutes (40.5%) and the subphylum Gamma-Proteobacteria (33.3%). The phylogenetic distance matrix results suggested that, out of 42 isolates, 37 were different strains of 19 known species,and that at least 6 strains represented 6 new species within 6 characterized genera. CONCLUSION: The results presented above showed that there were abundant species diversity and phylogenetic diversity of bacteria isolated from the sea anemone.

Arthrobacter halodurans sp. nov., a new halotolerant bacterium isolated from sea water.

A novel Gram-positive, halotolerant, non-sporulating, non-motile, catalase-positive, oxidase-negative and aerobic bacterium, designated strain JSM 078085(T), was isolated from sea water collected from the South China Sea. Strain JSM 078085(T) exhibited a rod-coccus growth cycle and produced a yellow pigment. The strain was able to grow in the presence of 0-12% (w/v) NaCl and at pH 6.0-9.5 and 4-35 degrees C; optimum growth was observed at pH 7.0 and 25-30 degrees C in the absence of NaCl. The peptidoglycan type was A4alpha (L: -Lys-L: -Ala-L: -Glu). Cell-wall sugars contained galactose and glucose. Strain JSM 078085(T) contained menaquinone MK-9(H(2)) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as the major polar lipids. The major cellular fatty acids were anteiso-C(15:0), iso-C(15:0) and anteiso-C(17:0) and the DNA G + C content was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 078085(T) should be assigned to the genus Arthrobacter, being most closely related to the type strain of Arthrobacter rhombi (sequence similarity 97.1%), and the two strains formed a distinct lineage in the phylogenetic tree. The level of DNA-DNA relatedness between strain JSM 078085(T) and the type strain of Arthrobacter rhombi was 10.6%. The combination of phylogenetic analysis, DNA-DNA relatedness, phenotypic characteristics and chemotaxonomic data supported the view that strain JSM 078085(T) represents a novel species of the genus Arthrobacter, for which the name Arthrobacter halodurans sp. nov. is proposed. The type strain is JSM 078085(T) (=DSM 21081(T)=KCTC 19430(T)).